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- PDB-1siu: KUMAMOLISIN-AS E78H MUTANT -

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Basic information

Entry
Database: PDB / ID: 1siu
TitleKUMAMOLISIN-AS E78H MUTANT
Componentskumamolisin-As
KeywordsHYDROLASE / E78H
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family ...Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAlicyclobacillus sendaiensis (bacteria)
MethodX-RAY DIFFRACTION / DIRECT REFINEMENT / Resolution: 2.31 Å
AuthorsLi, M. / Wlodawer, A. / Gustchina, A. / Tsuruoka, N. / Ashida, M. / Minakata, H. / Oyama, H. / Oda, K. / Nishino, T. / Nakayama, T.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity
Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Tsuruoka, N. / Ashida, M. / Minakata, H. / Oyama, H. / Oda, K. / Nishino, T. / Nakayama, T.
History
DepositionMar 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: kumamolisin-As
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8643
Polymers36,7271
Non-polymers1362
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.160, 45.040, 49.430
Angle α, β, γ (deg.)114.82, 106.36, 102.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein kumamolisin-As


Mass: 36727.391 Da / Num. of mol.: 1 / Mutation: E78H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus sendaiensis (bacteria)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GB88
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 8000, Ammonium Sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 16, 2003 / Details: OSMIC
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. all: 12280 / Num. obs: 12280 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rsym value: 0.043 / Net I/σ(I): 17
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 6.1 / Rsym value: 0.118 / % possible all: 80.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXLrefinement
SHELXL-97refinement
RefinementMethod to determine structure: DIRECT REFINEMENT
Starting model: WILD-TYPE KUMAMOLISIN-AS APOENZYME

Resolution: 2.31→10 Å / Num. parameters: 10863 / Num. restraintsaints: 10637 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2866 607 5.3 %RANDOM
all0.1619 11509 --
obs0.1591 11509 89.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2712
Refinement stepCycle: LAST / Resolution: 2.31→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 6 177 2711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0189
X-RAY DIFFRACTIONs_zero_chiral_vol0.019
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.026
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.09
X-RAY DIFFRACTIONs_approx_iso_adps0

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